User: Dattatray Mongad

Reputation:
340
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Trusted
Location:
National Centre for Cell Science, Pune
Website:
http://www.nccs.res.in/
Twitter:
DattatrayMongad
Last seen:
3 days, 5 hours ago
Joined:
3 years, 2 months ago
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d************@gmail.com

Posts by Dattatray Mongad

<prev • 60 results • page 1 of 6 • next >
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Answer: A: how to download cazy database
... Don't know about cazy but I have used [dbCAN][1] which you can download also. [1]: http://bcb.unl.edu/dbCAN2/ ...
written 4 months ago by Dattatray Mongad340
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Answer: A: How To Extract The Core Genes From The Orthomcl Output File?
... Use this code [parseOrthoMCLOutput.py][1]. It will generate all core, accessory and uniq genes fasta files. [1]: https://github.com/drdee255/code-Util/blob/master/parseOrthoMCLOutput.py ...
written 4 months ago by Dattatray Mongad340
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Answer: A: what is the best method (normalization) to compare RNA-Seq samples from differen
... Yes you can do PCA using TPM values and TMM has been widely used as normalization technique for transcriptome data. You can use [DESeq2][1] [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 9 months ago by Dattatray Mongad340
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Answer: A: Can't make program in Python to read FASTA
... **use biopython:** from Bio import SeqIO for records in SeqIO.Parse("fastaFileName","fasta"): print( records.id ) print( records.seq ) ...
written 11 months ago by Dattatray Mongad340 • updated 11 months ago by h.mon28k
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Answer: A: compare expression between the same gene in different organisms?
... In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or ...
written 11 months ago by Dattatray Mongad340
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Answer: A: Metabolic pathways from list of protein ID numbers
... The server or tool depend on your protein ids. If its UniProt ids, then you can use UniProt id conversion tool and convert them to KEGG ids. Then use KeggMapper to get the list of pathways involved. You can follow typical gene enrichmnet analysis also. ...
written 12 months ago by Dattatray Mongad340
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Answer: A: What is microbiome community structure?
... Core means, bacterial OTU/genera present in all samples or individuals. To do core microbiome analysis please see this [tutorial][1] [1]: https://microbiome.github.io/microbiome/Core.html ...
written 12 months ago by Dattatray Mongad340
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Answer: A: Gut microbe annotation DB
... I am assuming you are using amplicon sequencing approach. Currently, there is not tool or database which can tell you all information at once. Bu you can play around to gather such information. 1. Use [PICRUSt][1], to discover genes present in your data and their abundances (in terms of KO and CO ...
written 12 months ago by Dattatray Mongad340
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Answer: A: gff3 to gtf conversion
... See previous posts here [45791][1] [1]: https://www.biostars.org/p/45791/ ...
written 12 months ago by Dattatray Mongad340
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Comment: C: Amino Acid matrices freely downloadable url
... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there. [1]: http://www.drive5.com/pop/VTML200I ...
written 13 months ago by Dattatray Mongad340

Latest awards to Dattatray Mongad

Popular Question 3 months ago, created a question with more than 1,000 views. For Genome annotation to KEGG KO ids
Scholar 4 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Scholar 9 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 12 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 15 months ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di

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